Current Research - Imaging & BioInformatics LIACS Leiden University

Imaging & BioInformatics Current Research Themes & Projects

Here we list the projects that we are currently involved in and or working on. For each of the projects a short introdution is given. More information can be obtained by following the given link(s). In the research projects section detailed information on a number of specific projects is given.

3D Imaging of development in zebrafish

A number of projects concern the 3D imaging of development in the zebrafish model system. 3D imaging offers us challenges in the manipulation of large numbers of 3D data as well as the integration of different types of 3D microscopy data, i.e. images. We work with Confocal and MultiPhoton Microscopy, serial sections (atlas) and Magnetic Resonance Microscopy (MRM).

Atlas of zebrafish development

Using optimized serial sections with our acquisition set-up for 3D reconstruction we have assembled a 3D atlas of the development of the zebrafish. This is to be used for the 3D annotation of patterns of gene expression. Detailed information can be found on our Atlas-pages.

Linking & Mining Spatiotemporal databases

We are currently assembling 3D patterns of gene expression to be able to do a 3D mapping. Databases that consitute a Gene Expression Management System (GEMS) are set up for this purpose. The GEMS links with standardized and enriched ontologies as well as the 3D atlas system for spatial reference.


Ontologies provide a powerfull mechanism in the process of annotation and this is important in all database projects that we are involved in. We started working with controlled vocabularies for developmental anatomy; this is now transposed to ontology.

3D reconstruction from serial sections

3D reconstruction from serial sections has been an interest in our research group for a long period of time. It goes hand in hand with 3D imaging of all kinds of microscpopical modalities. We have designed and implemented dedicated software for 3D reconstruction from plan parallel sections. Detailed discussions and galleries can be viewed in the 3D-imaging section.

Image Databases

Managing large collections of images is one of the key topics of our research group. All of our projects are concerned with the acquisition of large collections that need to be processed and/or made available for image retrieval. We focus on the image management in the acquisition phase as well as setting up virtual communities for which image exchange is important. Examples of such communities are the Cyttron project and the ZF-models project. Recently, we have developed the ImageDataBase for eXchange (IDBx).

Human Computer Interaction and Cognitive modelling

Understanding the user interface and use design principles in our products is crucial. In addition to student projects in Human Computer Interaction we are involved in modelling cognition and emotion using adaptive simulated agents.

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